Protocols-4pub
Reusable code collection
26 April, 2021
Multi-omics analysis protocols concluded by SajuukLyu [email protected].
声明：该项目仅供学习用途，请共同遵守开源协议，禁止用于商业盈利。未经作者同意请勿转载至其它媒体。
Integrated step-by-step vignettes present on the wiki.
These files including three main parts:
-
Preprocess pipeline (etc. bulkRNA, bulkATAC, ChIP, WGBS ...)
These R scripts are designed to generate a directory tree containing ordered directories for intermediate data and Linux bash scripts for each step. In convenient to submit jobs to different nodes of a computer cluster at same time, commands for multiple samples can be divided to several batches and than submit together.
-
Downstream analysis script (etc. DEG, GO, GSEA ...)
These scripts are the framework of different analyses designed to cope with the most simple scene of biology analysis.
-
Visualization script (etc. heatmap, PCA plot, Venn plot, track plot ...)
These scripts can generate some plots suitable for articles with very few post processing.
File description
- Preprocess pipeline
| file name | description |
|---|---|
| bulkATACpre.R | Preprocess pipelines for bulk ATAC-seq (vignettes) |
| bulkRNApre.R | Preprocess pipelines for bulk RNA-seq (vignettes) |
| ChIPpre.R | Preprocess pipelines for ChIP-seq |
| WGBSpre.R | Preprocess pipelines for Whole Genome Bisulfite Sequencing |
- Downstream analysis script
| file name | omics | description |
|---|---|---|
| downloadData.R | any | Download data from public databases |
| bulkRNAana_1_loadCount.R | RNA | Load multiple results and convert to count matrix |
| bulkRNAana_2a_DESeq.R | RNA | Perform DESeq analysis (for sample without replicate) |
| bulkRNAana_2b_DESeq2.R | RNA | Perform DESeq2 analysis (for sample with replicates) |
| bulkRNAana_3_GO.R | RNA | Perform GO analysis |
| bulkATACana_1_QC.R | ATAC | Quality control |
| bulkATACana_2_loadCount.R | ATAC | Load data and convert to peak matrix |
| bulkATACana_3_annotatePeak.R | ATAC | Annotate peaks to nearest genes |
| bulkATACana_4_GO.R | ATAC | Perform GO analysis |
| bulkATACana_5_peakTF.R | ATAC | Perform gene regulate network analysis |
- Visualization script
| file name | omics | description |
|---|---|---|
| Visulz_bulkRNA_PCA.R | RNA | PCA plot for samples |
| Visulz_bulkRNA_MAplot.R | RNA | MA plot for DEGs between group of samples |
| Visulz_bulkRNA_volcano.R | RNA | Volcano plot for DEGs between group of samples |
| Visulz_bulkRNA_heatmap.R | RNA | Heatmap of given genes for samples |
| Visulz_bulkRNA_GO.R | RNA | GO plot for DEGs |
| Visulz_bulkATAC_trackPlot.R | ATAC | Track plot for samples |
| Visulz_bulkATAC_PCA.R | ATAC | PCA plot for samples |
| Visulz_bulkATAC_heatmapPeak.R | ATAC | Heatmap of given peaks for samples |
| Visulz_bulkATAC_heatmapTrack.R | ATAC | Heatmap of given peak tracks for samples |
| Visulz_bulkATAC_peakAnnoDisp.R | ATAC | Histogram for peak annotation distribution |
| Visulz_bulkATAC_motifEnrich.R | ATAC | Scatter plot for enriched TFs for peak sets |
| Visulz_bulkATAC_network.R | ATAC | Network plot for peak sets |
Pipeline
- bulk RNA-seq
- bulk ATAC-seq
- ChIP-seq
- WGBS
